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Dehghan Z, Mirmotalebisohi SA, Mozafar M, Sameni M, Saberi F, Derakhshanfar A, Moaedi J, Zohrevand H, Zali H. Deciphering the similarities and disparities of molecular mechanisms behind respiratory epithelium response to HCoV-229E and SARS-CoV-2 and drug repurposing, a systems biology approach. Daru 2024; 32:215-235. [PMID: 38652363 PMCID: PMC11087451 DOI: 10.1007/s40199-024-00507-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/08/2024] [Indexed: 04/25/2024] Open
Abstract
PURPOSE Identifying the molecular mechanisms behind SARS-CoV-2 disparities and similarities will help find new treatments. The present study determines networks' shared and non-shared (specific) crucial elements in response to HCoV-229E and SARS-CoV-2 viruses to recommend candidate medications. METHODS We retrieved the omics data on respiratory cells infected with HCoV-229E and SARS-CoV-2, constructed PPIN and GRN, and detected clusters and motifs. Using a drug-gene interaction network, we determined the similarities and disparities of mechanisms behind their host response and drug-repurposed. RESULTS CXCL1, KLHL21, SMAD3, HIF1A, and STAT1 were the shared DEGs between both viruses' protein-protein interaction network (PPIN) and gene regulatory network (GRN). The NPM1 was a specific critical node for HCoV-229E and was a Hub-Bottleneck shared between PPI and GRN in HCoV-229E. The HLA-F, ADCY5, TRIM14, RPF1, and FGA were the seed proteins in subnetworks of the SARS-CoV-2 PPI network, and HSPA1A and RPL26 proteins were the seed in subnetworks of the PPI network of HCOV-229E. TRIM14, STAT2, and HLA-F played the same role for SARS-CoV-2. Top enriched KEGG pathways included cell cycle and proteasome in HCoV-229E and RIG-I-like receptor, Chemokine, Cytokine-cytokine, NOD-like receptor, and TNF signaling pathways in SARS-CoV-2. We suggest some candidate medications for COVID-19 patient lungs, including Noscapine, Isoetharine mesylate, Cycloserine, Ethamsylate, Cetylpyridinium, Tretinoin, Ixazomib, Vorinostat, Venetoclax, Vorinostat, Ixazomib, Venetoclax, and epoetin alfa for further in-vitro and in-vivo investigations. CONCLUSION We suggested CXCL1, KLHL21, SMAD3, HIF1A, and STAT1, ADCY5, TRIM14, RPF1, and FGA, STAT2, and HLA-F as critical genes and Cetylpyridinium, Cycloserine, Noscapine, Ethamsylate, Epoetin alfa, Isoetharine mesylate, Ribavirin, and Tretinoin drugs to study further their importance in treating COVID-19 lung complications.
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Affiliation(s)
- Zeinab Dehghan
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Amir Mirmotalebisohi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Mozafar
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Marzieh Sameni
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Saberi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amin Derakhshanfar
- Department of Comparative Biomedical Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Javad Moaedi
- Center of Comparative and Experimental Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Zohrevand
- Student Research Committee, Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biomedical Engineering and Medical Physics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hakimeh Zali
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Rai P, Marano JM, Kang L, Coutermarsh-Ott S, Daamen AR, Lipsky PE, Weger-Lucarelli J. Obesity fosters severe disease outcomes in a mouse model of coronavirus infection associated with transcriptomic abnormalities. J Med Virol 2024; 96:e29587. [PMID: 38587204 DOI: 10.1002/jmv.29587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/15/2024] [Accepted: 03/25/2024] [Indexed: 04/09/2024]
Abstract
Obesity has been identified as an independent risk factor for severe outcomes in humans with coronavirus disease 2019 (COVID-19) and other infectious diseases. Here, we established a mouse model of COVID-19 using the murine betacoronavirus, mouse hepatitis virus 1 (MHV-1). C57BL/6 and C3H/HeJ mice exposed to MHV-1 developed mild and severe disease, respectively. Obese C57BL/6 mice developed clinical manifestations similar to those of lean controls. In contrast, all obese C3H/HeJ mice succumbed by 8 days postinfection, compared to a 50% mortality rate in lean controls. Notably, both lean and obese C3H/HeJ mice exposed to MHV-1 developed lung lesions consistent with severe human COVID-19, with marked evidence of diffuse alveolar damage (DAD). To identify early predictive biomarkers of worsened disease outcomes in obese C3H/HeJ mice, we sequenced RNA from whole blood 2 days postinfection and assessed changes in gene and pathway expression. Many pathways uniquely altered in obese C3H/HeJ mice postinfection aligned with those found in humans with severe COVID-19. Furthermore, we observed altered gene expression related to the unfolded protein response and lipid metabolism in infected obese mice compared to their lean counterparts, suggesting a role in the severity of disease outcomes. This study presents a novel model for studying COVID-19 and elucidating the mechanisms underlying severe disease outcomes in obese and other hosts.
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Affiliation(s)
- Pallavi Rai
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
| | - Jeffrey M Marano
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, Virginia, USA
| | - Lin Kang
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Biomedical Affairs and Research, Edward Via College of Osteopathic Medicine, Monroe, Louisiana, USA
- College of Pharmacy, University of Louisiana Monroe, Monroe, Louisiana, USA
| | - Sheryl Coutermarsh-Ott
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
| | | | | | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD College of Veterinary Medicine, Blacksburg, Virginia, USA
- Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, Virginia, USA
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SALİHOĞLU R, SARAÇOĞLU F, SİBAİ M, ZENGİN T, ABAK MASUD B, KARASOY O, SÜZEK T. CompCorona: A web application for comparative transcriptome analyses of coronaviruses reveals SARS-CoV-2-specific host response. Turk J Biol 2023; 47:393-405. [PMID: 38681774 PMCID: PMC11045204 DOI: 10.55730/1300-0152.2673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/28/2023] [Accepted: 12/15/2023] [Indexed: 05/01/2024] Open
Abstract
Background/aim Understanding the mechanism of host transcriptomic response to infection by the SARS-CoV-2 virus is crucial, especially for patients suffering from long-term effects of COVID-19, such as long COVID or pericarditis inflammation, potentially linked to side effects of the SARS-CoV-2 spike proteins. We conducted comprehensive transcriptome and enrichment analyses on lung and peripheral blood mononuclear cells (PBMCs) infected with SARS-CoV-2, as well as on SARS-CoV and MERS-CoV, to uncover shared pathways and elucidate their common disease progression and viral replication mechanisms. Materials and methods We developed CompCorona, the first interactive online tool for visualizing gene response variance among the family Coronaviridae through 2D and 3D principal component analysis (PCA) and exploring systems biology variance using pathway plots. We also made preprocessed datasets of lungs and PBMCs infected by SARS-CoV-2, SARS-CoV, and MERS-CoV publicly available through CompCorona. Results One remarkable finding from the lung and PBMC datasets for infections by SARS-CoV-2, but not infections by other coronaviruses (CoVs), was the significant downregulation of the angiogenin (ANG) and vascular endothelial growth factor A (VEGFA) genes, both directly involved in epithelial and vascular endothelial cell dysfunction. Suppression of the TNF signaling pathway was also observed in cells infected by SARS-CoV-2, along with simultaneous activation of complement and coagulation cascades and pertussis pathways. The ribosome pathway was found to be universally suppressed across all three viruses. The CompCorona online tool enabled the comparative analysis of 9 preprocessed host transcriptome datasets of cells infected by CoVs, revealing the specific host response differences in cases of SARS-CoV-2 infection. This included identifying markers of epithelial dysfunction via interactive 2D and 3D PCA, Venn diagrams, and pathway plots. Conclusion Our findings suggest that infection by SARS-CoV-2 might induce pulmonary epithelial dysfunction, a phenomenon not observed in cells infected by other CoVs. The publicly available CompCorona tool, along with the preprocessed datasets of cells infected by various CoVs, constitutes a valuable resource for further research into CoV-associated syndromes.
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Affiliation(s)
- Rana SALİHOĞLU
- Department of Bioinformatics, University of Würzburg, Würzburg,
Germany
- Department of Bioinformatics, Graduate School of Science and Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
| | - Fatih SARAÇOĞLU
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
| | - Mustafa SİBAİ
- Josep Carreras Leukaemia Research Institute (IJC), Badalona,
Spain
| | - Talip ZENGİN
- Department of Bioinformatics, Graduate School of Science and Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
- Department of Molecular Biology and Genetics, Faculty of Science, Muğla Sıtkı Koçman University, Muğla,
Turkiye
| | - Başak ABAK MASUD
- Department of Bioinformatics, Graduate School of Science and Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
| | - Onur KARASOY
- Department of Bioinformatics, Graduate School of Science and Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
| | - Tuğba SÜZEK
- Department of Bioinformatics, Graduate School of Science and Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
- Department of Computer Engineering, Faculty of Engineering, Muğla Sıtkı Koçman University, Muğla,
Turkiye
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Gao H, Wang S, Duan H, Wang Y, Zhu H. Biological analysis of the potential pathogenic mechanisms of Infectious COVID-19 and Guillain-Barré syndrome. Front Immunol 2023; 14:1290578. [PMID: 38115996 PMCID: PMC10728822 DOI: 10.3389/fimmu.2023.1290578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023] Open
Abstract
Background Guillain-Barré syndrome (GBS) is a medical condition characterized by the immune system of the body attacking the peripheral nerves, including those in the spinal nerve roots, peripheral nerves, and cranial nerves. It can cause limb weakness, abnormal sensations, and facial nerve paralysis. Some studies have reported clinical cases associated with the severe coronavirus disease 2019 (COVID-19) and GBS, but how COVID-19 affects GBS is unclear. Methods We utilized bioinformatics techniques to explore the potential genetic connection between COVID-19 and GBS. Differential expression of genes (DEGs) related to COVID-19 and GBS was collected from the Gene Expression Omnibus (GEO) database. By taking the intersection, we obtained shared DEGs for COVID-19 and GBS. Subsequently, we utilized bioinformatics analysis tools to analyze common DEGs, conducting functional enrichment analysis and constructing Protein-protein interaction networks (PPI), Transcription factors (TF) -gene networks, and TF-miRNA networks. Finally, we validated our findings by constructing the Receiver Operating Characteristic (ROC) curves. Results This study utilizes bioinformatics tools for the first time to investigate the close genetic relationship between COVID-19 and GBS. CAMP, LTF, DEFA1B, SAMD9, GBP1, DDX60, DEFA4, and OAS3 are identified as the most significant interacting genes between COVID-19 and GBS. In addition, the signaling pathway of NOD-like receptors is believed to be essential in the link between COVID-19 and GBS.
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Affiliation(s)
| | | | | | | | - Hui Zhu
- Department of Neurology, The First Teaching Hospital of Jilin University, Changchun, Jilin, China
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Elgohary S, Eissa RA, El Tayebi HM. Thymoquinone, a Novel Multi-Strike Inhibitor of Pro-Tumorigenic Breast Cancer (BC) Markers: CALR, NLRP3 Pathway and sPD-L1 in PBMCs of HR+ and TNBC Patients. Int J Mol Sci 2023; 24:14254. [PMID: 37762557 PMCID: PMC10531892 DOI: 10.3390/ijms241814254] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/19/2023] [Accepted: 06/25/2023] [Indexed: 09/29/2023] Open
Abstract
Breast cancer (BC) is not only a mass of malignant cells but also a systemic inflammatory disease. BC pro-tumorigenic inflammation has been shown to promote immune evasion and provoke BC progression. The NOD-like receptor (NLR) family pyrin domain-containing protein 3 (NLRP3) inflammasome is activated when pattern recognition receptors (PRRs) sense danger signals such as calreticulin (CALR) from damaged/dying cells, leading to the secretion of interleukin-1β (IL-1β). CALR is a novel BC biological marker, and its high levels are associated with advanced tumors. NLRP3 expression is strongly correlated with an elevated proliferative index Ki67, BC progression, metastasis, and recurrence in patients with hormone receptor-positive (HR+) and triple-negative BC (TNBC). Tumor-associated macrophages (TAMs) secrete high levels of IL-1β promoting endocrine resistance in HR+ BC. Recently, an immunosuppressive soluble form of programmed death ligand 1 (sPD-L1) has been identified as a novel prognostic biomarker in triple-negative breast cancer (TNBC) patients. Interestingly, IL-1β induces sPD-L1 release. BC Patients with elevated IL-1β and sPD-L1 levels show significantly short progression-free survival. For the first time, this study aims to investigate the inhibitory impact of thymoquinone (TQ) on CALR, the NLRP3 pathway and sPD-L1 in HR+ and TNBC. Blood samples were collected from 45 patients with BC. The effect of differing TQ concentrations for different durations on the expression of CALR, NLRP3 complex components and IL-1β as well as the protein levels of sPD-L1 and IL-1β were investigated in the peripheral blood mononuclear cells (PBMCs) and TAMs of TNBC and HR+ BC patients, respectively. The findings showed that TQ significantly downregulated the expression of CALR, NLRP3 components and IL-1β together with the protein levels of secreted IL-1β and sPD-L1. The current findings demonstrated novel immunomodulatory effects of TQ, highlighting its potential role not only as an excellent adjuvant but also as a possible immunotherapeutic agent in HR+ and TNBC patients.
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Affiliation(s)
- Sawsan Elgohary
- Clinical Pharmacology and Pharmacogenomics Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
| | - Reda A. Eissa
- Department of Surgery, Faculty of Medicine, Ain Shams University, Cairo 11591, Egypt;
| | - Hend M. El Tayebi
- Clinical Pharmacology and Pharmacogenomics Research Group, Department of Pharmacology and Toxicology, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt;
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O’Connor LM, O’Connor BA, Zeng J, Lo CH. Data Mining of Microarray Datasets in Translational Neuroscience. Brain Sci 2023; 13:1318. [PMID: 37759919 PMCID: PMC10527016 DOI: 10.3390/brainsci13091318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023] Open
Abstract
Data mining involves the computational analysis of a plethora of publicly available datasets to generate new hypotheses that can be further validated by experiments for the improved understanding of the pathogenesis of neurodegenerative diseases. Although the number of sequencing datasets is on the rise, microarray analysis conducted on diverse biological samples represent a large collection of datasets with multiple web-based programs that enable efficient and convenient data analysis. In this review, we first discuss the selection of biological samples associated with neurological disorders, and the possibility of a combination of datasets, from various types of samples, to conduct an integrated analysis in order to achieve a holistic understanding of the alterations in the examined biological system. We then summarize key approaches and studies that have made use of the data mining of microarray datasets to obtain insights into translational neuroscience applications, including biomarker discovery, therapeutic development, and the elucidation of the pathogenic mechanisms of neurodegenerative diseases. We further discuss the gap to be bridged between microarray and sequencing studies to improve the utilization and combination of different types of datasets, together with experimental validation, for more comprehensive analyses. We conclude by providing future perspectives on integrating multi-omics, to advance precision phenotyping and personalized medicine for neurodegenerative diseases.
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Affiliation(s)
- Lance M. O’Connor
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Blake A. O’Connor
- School of Pharmacy, University of Wisconsin, Madison, WI 53705, USA;
| | - Jialiu Zeng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
| | - Chih Hung Lo
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore;
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Chemical profile of anti-epidemic sachet based on multiple sample preparation coupled with gas chromatography-mass spectrometry analysis combined with an embedded peaks resolution method and their action mechanisms. J Chromatogr A 2023; 1691:463816. [PMID: 36716594 DOI: 10.1016/j.chroma.2023.463816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 01/22/2023]
Abstract
The anti-epidemic sachet (Fang Yi Xiang Nang, FYXN) in traditional Chinese medicine (TCM) can prevent COVID-19 through volatile compounds that can play the role of fragrant and dampness, heat-clearing and detoxifying, warding off filth and pathogenic factors. Nevertheless, the anti-(mutant) SARS-CoV-2 compounds and the compounds related to the mechanism in vivo, and the mechanism of FYXN are still vague. In this study, the volatile compound set of FYXN was constructed by gas chromatography-mass spectrometry (GC-MS) based on multiple sample preparation methods, which include headspace (HS), headspace solid phase microextraction (HS-SPME) and pressurized liquid extraction (PLE). In addition, selective ion analysis (SIA) was used to resolve embedded chromatographic peaks present in HS-SPME results. Preliminary analysis of active compounds and mechanism of FYXN by network pharmacology combined with disease pathway information based on GC-MS results. A total of 96 volatile compounds in FYXN were collected by GC-MS analysis. 39 potential anti-viral compounds were screened by molecular docking. 13 key pathways were obtained by KEGG pathway analysis (PI3K-Akt signaling pathway, HIF-1 signaling pathway, etc.) for FYXN to prevent COVID-19. 16 anti-viral compounds (C95, C91, etc.), 10 core targets (RELA, MAPK1, etc.), and 16 key compounds related to the mechanism in vivo (C56, C30, etc.) were obtained by network analysis. The relevant pharmacological effects of key pathways and key compounds were verified by the literature. Finally, molecular docking was used to verify the relationship between core targets and key compounds, which are related to the mechanism in vivo. A variety of sample preparation methods coupled with GC-MS analysis combined with an embedded peaks resolution method and integrated with network pharmacology can not only comprehensively characterize the volatile compounds in FYXN, but also expand the network pharmacology research ideas, and help to discover the active compounds and mechanisms in FYXN.
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Meng H, Wang S, Tang X, Guo J, Xu X, Wang D, Jin F, Zheng M, Yin S, He C, Han Y, Chen J, Han J, Ren C, Gao Y, Liu H, Wang Y, Jin R. Respiratory immune status and microbiome in recovered COVID-19 patients revealed by metatranscriptomic analyses. Front Cell Infect Microbiol 2022; 12:1011672. [PMID: 36483456 PMCID: PMC9724627 DOI: 10.3389/fcimb.2022.1011672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) is currently a severe threat to global public health, and the immune response to COVID-19 infection has been widely investigated. However, the immune status and microecological changes in the respiratory systems of patients with COVID-19 after recovery have rarely been considered. We selected 72 patients with severe COVID-19 infection, 57 recovered from COVID-19 infection, and 65 with non-COVID-19 pneumonia, for metatranscriptomic sequencing and bioinformatics analysis. Accordingly, the differentially expressed genes between the infected and other groups were enriched in the chemokine signaling pathway, NOD-like receptor signaling pathway, phagosome, TNF signaling pathway, NF-kappa B signaling pathway, Toll-like receptor signaling pathway, and C-type lectin receptor signaling pathway. We speculate that IL17RD, CD74, and TNFSF15 may serve as disease biomarkers in COVID-19. Additionally, principal coordinate analysis revealed significant differences between groups. In particular, frequent co-infections with the genera Streptococcus, Veillonella, Gemella, and Neisseria, among others, were found in COVID-19 patients. Moreover, the random forest prediction model with differential genes showed a mean area under the curve (AUC) of 0.77, and KCNK12, IL17RD, LOC100507412, PTPRT, MYO15A, MPDZ, FLRT2, SPEG, SERPINB3, and KNDC1 were identified as the most important genes distinguishing the infected group from the recovered group. Agrobacterium tumefaciens, Klebsiella michiganensis, Acinetobacter pittii, Bacillus sp. FJAT.14266, Brevundimonas naejangsanensis, Pseudopropionibacterium propionicum, Priestia megaterium, Dialister pneumosintes, Veillonella rodentium, and Pseudomonas protegens were selected as candidate microbial markers for monitoring the recovery of COVID patients. These results will facilitate the diagnosis, treatment, and prognosis of COVID patients recovering from severe illness.
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Affiliation(s)
- Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shuang Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xiaomeng Tang
- Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Guo
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Xinming Xu
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Dagang Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Fangfang Jin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaonan He
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jin Chen
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jinyu Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaobo Ren
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Yantao Gao
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Huifang Liu
- Translational R&D Center, Guangzhou Vision Medicals Co. LTD, Guangzhou, China
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China,*Correspondence: Yajie Wang, ; Ronghua Jin,
| | - Ronghua Jin
- Beijing Ditan Hospital, Capital Medical University, Beijing, China,*Correspondence: Yajie Wang, ; Ronghua Jin,
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